Carotenoid cleavage dioxygenases (CCDs) are enzymes that catalyze the oxidative cleavage of carotenoids at a specific double bond to generate apocarotenoids. In this study, we investigated the activity and substrate preferences of NSC3, a CCD of Nostoc sp. strain PCC 7120, in vivo and in vitro using natural and nonnatural carotenoid structures. NSC3 cleaved ␤-apo-8=-carotenal at 3 positions, C-13AC-14, C-15AC-15=, and C-13=AC-14=, revealing a unique cleavage pattern. NSC3 cleaves the natural structure of carotenoids 4,4=-diaponeurosporene, 4,4=-diaponeurosporen-4=-al, 4,4=-diaponeurosporen-4=-oic acid, 4,4=-diapotorulene, and 4,4=-diapotorulen-4=-al to generate novel cleavage products (apo-14=-diaponeurosporenal, apo-13=-diaponeurosporenal, apo-10=-diaponeurosporenal, apo-14=-diapotorulenal, and apo-10=-diapotorulenal, respectively). The study of carotenoids with natural or nonnatural structures produced by using synthetic modules could provide information valuable for understanding the cleavage reactions or substrate preferences of other CCDs in vivo and in vitro.